1. Field of the Invention
The present invention relates to a method of using artificial genes as controls in gene expression analysis systems. More particularly, the present invention relates to a method of producing Controls for use in gene expression analysis systems such as macroarrays, real-time PCR, northern blots, SAGE and microarrays, such as those provided in the Microarray ScoreCard system.
2. Description of Related Art
Gene expression profiling is an important biological approach used to better understand the molecular mechanisms that govern cellular function and growth. Microarray analysis is one of the tools that can be applied to measure the relative expression levels of individual genes under different conditions. Microarray measurements often appear to be systematically biased, however, and the factors that contribute to this bias are many and ill-defined (Bowtell, D. L., Nature Genetics 21, 25-32 (1999); Brown, P. P. and Botstein, D., Nature Genetics 21, 33-37 (1999)). Others have recommended the use of “spikes” of purified mRNA at known concentrations as controls in microarray experiments. Affymetrix includes several for use with their GeneChip products. In the current state of the art, these selected genes are actual genes selected from very distantly related organisms. For example, the human chip (designed for use with human mRNA) includes control genes from bacterial and plant sources. Affymetrix sells mRNA corresponding to these genes for spiking into the labeling reaction and inclusion in the hybridization reaction.
Each of the prior art controls includes transcribed sequences of DNA from some source. As a result, that source cannot be the subject of a hybridization experiment using those controls due to the inherent hybridization of the controls to its source. What is needed, therefore, is a set of controls which do not hybridize with the DNA of any source which may be the subject of an experiment. More desirably, there is a need for a control for gene expression analysis which does not hybridize with any known source.